SMTL ID : 6keh.1

Crystal structure of BRD4 bromodomain 1 (BD1) in complex with 6,16-dimethoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(17),3,5,7,9,13,15-heptaen-12-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.1: 2 residues within 4Å: Chain A: K.58, K.61 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.58, A:K.58, A:K.61 FMT.2: 5 residues within 4Å: Chain A: T.19, Q.21, N.80, A.81 Ligands: FMT.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.81 Water bridges: A:Q.21, A:Q.82 FMT.3: 4 residues within 4Å: Chain A: T.19, N.20, Q.21 Ligands: FMT.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.19, A:N.20, A:Q.21 FMT.4: 2 residues within 4Å: Chain A: N.121, E.122 No protein-ligand interaction detected (PLIP)

1 x D6R: 6,16-dimethoxy-11-methyl-2-oxa-11-azatetracyclo[8.6.1.03,8.013,17]heptadeca-1(17),3,5,7,9,13,15-heptaen-12-one(Non-covalent)

D6R.5: 9 residues within 4Å: Chain A: W.40, P.41, F.42, Q.44, V.46, L.51, Y.98, N.99, I.105 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:P.41, A:L.51, A:L.51, A:Y.98, A:I.105 Hydrogen bonds: A:N.99 Water bridges: A:Q.44 pi-Stacking: A:W.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yoo, M. et al., Synthesis and Structure-Activity Relationships of Aristoyagonine Derivatives as Brd4 Bromodomain Inhibitors with X-ray Co-Crystal Research. Molecules (2021)

Release Date

2020-07-08

Peptides

Bromodomain-containing protein 4: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Bromodomain-containing protein 4

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